OH, I see that there is a DO.db in bioconductor already:

http://www.bioconductor.org/help/bioc-views/release/data/annotation/html/DO.db.html

<http://www.bioconductor.org/help/bioc-views/release/data/annotation/html/DO.db.html>That
is great. However, it doesn't seem to install for me.

> biocLite("DO.db")
Using R version 2.11.1, biocinstall version 2.6.9.
Installing Bioconductor version 2.6 packages:
[1] "DO.db"
Please wait...

Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  argument 'lib' is missing: using
'/home/nmrp3/R/x86_64-pc-linux-gnu-library/2.11'
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘DO.db’ is not available

It looks like I have bioconductor 2.6 but DO.db is packaged for 2.7.

> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite()
Using R version 2.11.1, biocinstall version 2.6.9.
Installing Bioconductor version 2.6 packages:
[snip]

So it looks like I'm being handed bioconductor 2.6 rather than 2.7 - perhaps
this is because I allowed Ubuntu to install R version 2.11.1?

Matthew

On 5 March 2011 16:14, Matthew Pocock <turingatemyhamster@gmail.com> wrote:

> Hi,
>
> I've been using GO.db and find it very useful. I'd now like to have a
> similar API for the disease ontology (DO). Is there something I can read
> that may explain how to expose the DO data as a package? I guess I'm asking
> if there is a guide to how I would develop DO.db.
>
> Thanks,
>
> Matthew
>
> --
> Matthew Pocock
> mailto: turingatemyhamster@gmail.com
> gchat: turingatemyhamster@gmail.com
> msn: matthew_pocock@yahoo.co.uk
> irc.freenode.net: drdozer
> (0191) 2566550
>
>


-- 
Matthew Pocock
mailto: turingatemyhamster@gmail.com
gchat: turingatemyhamster@gmail.com
msn: matthew_pocock@yahoo.co.uk
irc.freenode.net: drdozer
(0191) 2566550

	[[alternative HTML version deleted]]

